Additional File 3
Supporting materials
Statistical Model
For each gene, let yij  yi (tij ) be the expression level of individual i measured at time t ij , where t ij is
the time when the j th measurement of the i th individual is obtained. Using the varying intercept
model14, yij is modeled by
yij   (tij )   i (tij ) ,
where  (t ) is the population average expression curve and  i (t ) is random error of individual i from
this curve at time t . Here  (t ) is approximated by a basis function expansion by
 (t )   s 0  s Bs (t ) ,
K
where Bs for s  0,..., K is a set of B-spline basis, and the least square basis estimator of  (t ) given by
ˆ (t )   s 0 ˆs Bs (t )
K
can be obtained by minimizing the sum of squares between ˆ (tij ) and yij 14.
To test whether there is a significant difference between the curves of ISR and non-ISR patients, a
goodness-of-fit test based on the comparison between the residual sum of squares under the null and
alternative hypothesis was considered. Under the null hypothesis, a single curve was fit using the
combined ISR and non-ISR patients, and the residual sum of squares from the least square fit, RSS0 , is
obtained. Two separate curves were fit for the ISR and non-ISR patients under the alternative hypothesis
and similarly the residual sum of squares, RSS1 , is obtained. The test statistic was then calculated as
T  ( RSS0  RSS1 ) / RSS1 .
The null distribution of this test statistic is assessed based on 10 million bootstrap samples obtained by
sampling a number of subjects as described in Huang, Wu and Zhou14.
List of probes identified in the CardioGene discovery analysis:
201222_s_at
217814_at
203276_at
218047_at
208374_s_at
209207_s_at
202502_at
203996_s_at
212803_at
201181_at
217758_s_at
214773_x_at
213389_at
203044_at
200084_at
218092_s_at
208857_s_at
216304_x_at
209345_s_at
203994_s_at
212411_at
213654_at
212460_at
221423_s_at
222294_s_at
203371_s_at
200821_at
221504_s_at
210849_s_at
212513_s_at
201223_s_at
218646_at
203605_at
204829_s_at
217886_at
221613_s_at
202654_x_at
218341_at
212016_s_at
220131_at
201807_at
221123_x_at
205126_at
215203_at
205202_at
201351_s_at
List of probes validated in the analysis of decode samples:
210849_s_at
209207_s_at
208857_s_at
208374_s_at
212411_at
209345_s_at
205202_at
203994_s_at
217886_at
220131_at
217758_s_at
217814_at
212513_s_at
202654_x_at
202502_at
216304_x_at
200821_at
201807_at
218092_s_at
201222_s_at
201351_s_at
218646_at
214773_x_at
203996_s_at
203371_s_at
203605_at
218047_at
212460_at
221123_x_at
212803_at
222294_s_at
205126_at
221504_s_at
201223_s_at
203276_at
204829_s_at